Persistent Identifier System Research Articles

Zen and the Art of Persistent Identifier Service Development for Digital Specimen

One of the most desired (and still missing) elements to enable the concept of Digital Extended (Webster et al. 2021) Specimens is a persistent identifier (PID) for the new digital specimen object. Digital Specimens are created to act as a digital surrogate of the physical objects. Digital Specimens contain all data relevant to the specimens as well as derived data like genetic sequences, trait information, and references to publications, species and environmental information. A PID for the Digital Specimen is thus essential to link it to the extended information. Furthermore, the extended information also needs PIDs to create unique and resolvable references to enable bidirectional linking. DiSSCo, Distributed System of Scientific Collections, has done extensive work to select the most appropriate PID scheme (Hardisty et al. 2021) and design a PID infrastructure for the pan-European specimen collections. The design was created in the Biodiversity Community Integrated Knowledge Library project (BiCIKL) with funding from the European Commission. The draft design has been discussed with technical specialists in the joint DiSSCo and Consortium of European Taxonomic Facilities (CETAF) community, with international stakeholders like GBIF and iDigBio. The draft was also presented at the 2022 conference of SPNHC (the Society for the Preservation of Natural History Collections) for further feedback, after which it was finalised. This talk will provide a short overview of the key elements in the design of the Persistent Identifier system for Digital Specimens such as the metadata schema, a human friendly string format, and PID lifecycle with support for state changes of the physical object such as splitting and merging. We will illustrate this by showing the current status of development. The Digital Specimen forms the backbone of the FAIR (Findable, Accessible, Interoperable, Reusable) services (Addink et al. 2021) in development by the DiSSCo Prepare project, a project to prepare for the new research infrastructure which currently involves 170 institutions in 23 countries holding an estimated 1,5 billion specimens. The Digital Specimen is a FAIR Digital Object with a PID and machine actionable metadata to make it FAIR. The PID service ensures the identifiers’ integrity and preserves these linkages, improving the FAIR quality of all specimen data. The talk will describe the system design and current test deployment setup, as well as delve into a few technical details of the Handle Server architecture, PID Kernel records, and a roadmap for the service development. The design and test work are done under the auspices of the BiCIKL project that aims to foster collaboration between infrastructures and develop bidirectional connections between the data so that they become part of a big FAIR data pool seamlessly available to researchers (Penev et al. 2022).

The DiSSCo Knowledgebase: A trusted information hub for the natural science collection community worldwide

In the last two decades, various projects and initiatives have conducted research on how to share, exchange, and link information from natural science collection objects. This profound (technical) knowledge, standards, tools, and best practices are essential to the development of any new research infrastructure facilitating research on bio- and geodiversity. However, the knowledge and research results are usually not easily accessible at a single point and particularly not in a well-curated form. Here, the Knowledgebase developed for the Distributed System of Scientific Collections (DiSSCo) comes into play. This information hub will act as trusted source for project outcomes and other relevant resources (e.g., web services, Persistent Identifier Systems, controlled vocabularies, domain-specific ontologies and standards) for users and developers of DiSSCo and other research infrastructures worldwide. In this talk, we will present the current version of the DiSSCo Knowledgebase, its developmental approach, and the opportunity for this source to act as an e-service for various stakeholder groups interested in and working with natural science collections worldwide.

Open Science—A Question of Trust

Collaboration and the sharing of knowledge is at the heart of Open Science (OS). However, we need to know that the knowledge we find and share is really what it purports to be; and we need to know that the authors we hope to collaborate with are really the people they claim to be. In this paper, the author argues that a prerequisite for OS is trust and that persistent identifiers help to build that trust. The persistent identifier systems must themselves be trustworthy and they must be able to connect the user or their machine to the information they need now and into the future. Infrastructure is rather like plumbing: It goes unnoticed and unappreciated until it fails. This paper puts infrastructure for persistent identifiers in the spotlight as a core component of OS.

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL: www.kimosys.org

A blockchain based Trusted Persistent Identifier system for Big Data in Science

Abstract A stable reference of Internet resources is crucial not only to identify a resource in a trustworthy and certified way but also to guarantee continuous access to it over time. The current practice in scientific publication as the use of a Persistent Identifier (PID) like a DOI or Handle, is becoming attractive also for the datasets. In fact, in the era of Big Data, the aspects of replicability and verification of the scientific result are paramount. In this paper we verify the functional feasibility of permissioned blockchain technology as a tool to implement a Trustworthy Persistent Identifier (T-PID) system for datasets in the scientific domain.

Persistent, Global, Unique: The three key requirements for a trusted identifier system for physical samples

There is growing recognition that unambiguous citation and tracking of physical samples allows previously impossible linking of samples to data and publications, linking and integration of sample-based observations across data systems, and paves the road towards advanced data mining of sample-based data. And in recent years, there has been an uptake in the use of Persistent Identifiers (PIDs) for physical samples to support such citation and tracking. The IGSN (International Geo Sample Number) is a PID for physical samples. It was originally developed for the solid earth sciences, and has evolved into an international PID system with members in five continents and a network of active allocating agents. It has been adopted by a growing number and range of stakeholders worldwide, including national geological surveys, research infrastructure providers, collection curators, researchers, and data managers, and by other disciplines that need to refer to physical samples. Nearly 6.9 million samples have been registered with IGSNs so far. The IGSN system uses the Handle System (Kahn and Wilensky 1995; see also Handle.Net®) and has an international organization, IGSN e.V., to manage its governance structure and the technical architecture. The recent expansion of the IGSN beyond the geosciences into other domains such as biodiversity, archeology, and material sciences confirms the power of its concept and implementation, but imposes substantial pressures on the existing capacity and capabilities of the IGSN architecture and its governing organization. Modifications to the IGSN organizational and technical architecture are necessary at this point to keep pace with the growing demand and expectations. These changes are also necessary to ensure trustworthy and sustainable services for PID registration and resolution in a maturing research data ecosystem. The essential criteria for a trustworthy system include an organizational foundation that ensures longevity, sustainability, proper governance, and regular quality assessment of registration services. It also includes a reliable and secure technical platform, based on open standards, which is sufficiently scalable and flexible to accommodate the growing diversity of specimen types, use cases, and stakeholder requirements. In 2018, a major planning project for the IGSN was funded by the Alfred P. Sloan Foundation. An international group of experts participates in re-designing and improving the existing organization and technical architecture of the IGSN system, revising the current business model of the IGSN e.V. and professionalizing its operations. The goal is for the IGSN system to be able to respond to, and support in a sustainable manner, the rapidly growing demands of a global and increasingly multi-disciplinary user community, and to ensure that the IGSN will be a trustworthy, stable, and adaptable persistent identifier system for material samples, both technically and organizationally. The end result should also satisfy and facilitate participation across research domains, and will be a reliable component of the evolving research data ecosystem. Finally, it will ensure that the IGSN is recognized as a trusted partner by data infrastructure providers and the science community alike.

Decentralized Persistent Identifiers: a basic model for immutable handlers

Persistent Identifier (PID) systems have evolved in the last decade to mitigate the problem of link rot and provide unique and resolvable identifiers for digital objects, becoming a key element in archival services. However, they still depend on centralized services which may either become unavailable or cease to behave or be managed as expected. Decentralized technologies may serve as the infrastructure for the design of a trustless PID system over which other incentive mechanisms may be devised. Here we discuss a basic model for such a novel PID system, based on the capacity of content addressing of current decentralized file systems and the concept and definition of verifiable claims as metadata statements about the existence of an immutable digital resource. An example basic design is described using the Interplanetary File System (IPFS) as supporting infrastructure with a minimal set of conventions, that could be used as an alternate mechanism for storage of byte streams in digital repositories as DSpace or CKAN.

The Challenge of Ensuring Persistency of Identifier Systems in the World of Ever-Changing Technology

The identification of information objects has always been important with library collections with indexes having been created in the most ancient times. Since the digital age, many specialised and generic persistent identifier (PID) systems have been used to identify digital objects. Just as many ancient indexes have died over time, so too PID systems have had a lifecycle from inception to active phase to paralysis, and eventually a fall into oblivion. Where the indexes within the Great Library at Alexandria finally succumbed to fire, technology change has been the destroyer of more recent digital indexes. We distil four PID system design principles from observations over the years that we think should be implemented by PID system architects to ensure that their systems survive change. The principles: describe how to ensure identifiers’ system and organisation independence; codify the delivery of essential PID system functions; mandate a separation of PID functions from data delivery mechanisms; and require generation of policies detailing how change is handled. In addition to suggesting specific items for each principle, we propose that a platform-independent model (PIM) be established for persistent identifiers – of any sort and with any resolver technology – in order to enable transition between present and future systems and the preservation of the identifiers’ functioning. We detail our PID system—the PID Service—that implements the proposed principles and a data model to some extent and we describe an implementation case study of an organisation’s implementation of PID systems that implement the Pillars further but still not completely. Penultimately, we describe in a Future Work section, an opportunity for the use of both the Pillars and the PIM; that of the World Wide Web Consortium’s Permanent Identifier Community Group who is seeking to “set up and maintain a secure permanent, URL re-direction service for the web”.

20 Years of Persistent Identifiers – Which Systems are Here to Stay?

Web-based persistent identifiers have been around for more than 20 years, a period long enough for us to start observing patterns of success and failure. Persistent identifiers were invented to address challenges arising from the distributed and disorganised nature of the internet, which often resulted in URLs to internet endpoints becoming invalid. Over the years several different persistent identifier systems have been applied to the identification of research data, not all with the same level of success in terms of uptake and sustainability. We investigate the uptake of persistent identifier systems and discuss the factors that might determine the stability and longevity of these systems. Persistent identifiers have become essential elements of global research data infrastructures. Understanding the factors that influence the stability and longevity of persistent identifier systems will help us guide the future development of this important element of research data infrastructures and will make it easier to adapt to future technological and organisational changes.

Revision of the URN standards

This paper provides a short overview of the on-going revision of the uniform resource names (URN) standard base, and its implications to other persistent identifier systems (PIDs), cool uniform resource identifiers (URIs) and URI generic syntax.